What Can Sockeye Do

Full features 3D browser

  • Versatile, state of the art 3D workspace, optimized for fast data access, visual and computational analysis.

Access multiple data sources

  • Ensembl
  • GFF Files
  • Transfac
  • Jaspar
  • GSC internal coexpression database
  • Output files from several motif discovery programs
  • NHGRI Encode: Encyclopedia of DNA elements project
  • Crosslink information to
    • Wormbase
    • Geneview (EnsEMBL)

Work out Relationships between genomic features

  • Functional relationsships, like homology, orthology, cooexpression etc
  • Relationships based on genomic locations, thus allowing to answer questions like
    • "show me all scan results that fall into coding regions"?
    • "show me all discovered motifs that are located withing CPG islands"?
    • "which of these binding sites fall within the 3000 base upstream region of the closest gene"?


  • Extremely powerfull and generic alignment postprocessing including various smoothing methods and statistical analysis
  • For complete list of alignment algorithms supported by Sockeye, please view Algorithms page

Motif discovery

  • Multiple flexible postprocessing methods based on feature sets allows for quick problem specific assesment of the relevance of the discovered featured
  • For complete list of motif discovery algorithms supported by Sockeye, please view Algorithms page

Sequence scanning and analysis

  • Scan with PWMs or sequence motifs
    • using PWMs TRANSFAC or JASPAR
    • using PWMs generated by various discovery programs
    • using custom PWMs
    • specifying a consensus string and number of mismatches
    • work with masked or unmasked sequences
  • Analyse the information content of a sequence or part of a sequence

Primer prediction

Page last modified Feb 06, 2007